It doesn't discredit anything. Sometimes what you care about is performance from cold start. Serverless And CLIs for example. JIT aint gonna help you there , and this problem falls into that category.
EDIT: did you read the article? It is not a microbenchmark.
If you want a fast cli and java, you'd have the java process running and feed the input/output where by some means. Overall Java is not a good fit for a classic CLI, at least not with the JIT - it works in a pinch of course but it's well known it has a slow bootstrap.
Of course I read the article, the benchmarks are at the end. The rest is about LoC (which is yet another benchmark, albeit even more useless). I even read all the code on github, there is a room for improvement there as well.
EDIT: did you read the article? It is not a microbenchmark.